rs4964513

chr12-106981980-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001033050.3(MTERF2):c.-58+3135A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,164 control chromosomes in the GnomAD database, including 2,027 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.14 (2027 hom., cov: 32)
• Consequence: MTERF2 NM_001033050.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.537

Genes affected

MTERF2 (HGNC:30779): (mitochondrial transcription termination factor 2) Enables DNA binding activity. Predicted to be involved in termination of mitochondrial transcription. Located in mitochondrion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTERF2	NM_001033050.3	c.-58+3135A>G		intron_variant		ENST00000240050.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTERF2	ENST00000240050.9	c.-58+3135A>G		intron_variant		1	NM_001033050.3	P1

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20778 AN: 152046 Hom.: 2026 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.0983

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0595

Gnomad OTH AF: 0.132

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.137 AC: 20803 AN: 152164 Hom.: 2027 Cov.: 32 AF XY: 0.140 AC XY: 10396 AN XY: 74414

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.0983

Gnomad4 EAS AF: 0.252

Gnomad4 SAS AF: 0.129

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.0595

Gnomad4 OTH AF: 0.134

Alfa AF: 0.0770 Hom.: 620

Bravo AF: 0.143

Asia WGS AF: 0.211 AC: 732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	3.5
Dann	Benign	0.84

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4964513; hg19: chr12-107375758;